Numerous non-coding RNAs such lncRNAs, snRNAs, circRNAs or miRNAs are constantly identified hence their functional characterization is of great importance.
Learn how current aptamer-based RNA imaging and analysis strategies contribute to characterization of a specific RNA.
RNA aptamers are specific RNA sequences that can be detected by small-molecule dyes. Dye fluorescence is significantly enhanced upon complex formation thus aptamers are versatile tags for imaging and functional analysis of coding and non-coding RNA both in vitro and in live cells[1-4] (Tab. 1). Attachement of a specific aptamer sequence to a RNA of interest can be performed e.g. by in vitro transcription.
Table 1: Application of light-up aptamers in imaging & analysis of coding and non-coding RNA.
|RNA Target||Application||Aptamer/Dye Combination||Ref.|
|mRNA||Live cell imaging (E. coli) of specific endogenous mRNA||Spinach derivative/DFHBI|||
|Live cell imaging (mammalian cells) of specific endogenous mRNA||Broccoli & Spinach derivatives/DFHBI-1T|||
|lncRNA||Live cell imaging (mammalian cells) of aptamer-tagged lncRNA||Broccoli derivative/DFHBI-1T|||
|miRNA||miRNA detection in vitro||Spinach derivative/DFHBI|||
|snoRNA||Live cell imaging (yeast) of aptamer-tagged snoRNA||Broccoli derivative/DFHBI-1T|||
|tRNA||Live cell imaging (E. coli) of ribosome activity||Spinach derivative/DFHBI|||
|snoRNA/tRNA/5S RNA||Live cell imaging (mammalian cells) and quantification of transcription||Corn/DFHO|||
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 George et al. (2018) Intracelluar RNA-tracking methods. Open Biol 8:180104.
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 Ong et al. (2017) Live cell imaging of endogenous mRNA using RNA-based Fluorescence „Turn-On“ Probe. ACS Chem Biol 12 (1):200.
 Wang et al. (2019) Visualizing mRNA in live mammalian cells. Methods 2023 (18):30287.
 O‘Leary et al. (2017) Long non-coding RNA PARTICLEbridges histone and DNA methylation SCIENTIFIC Reports 7:1790.
 Zhou et al. (2019) Cascade transcription amplification of RNA aptamer for ultrasensitive microRNA detection. Anal. Chem. 91:5295.
 Ying et al. (2018) Spinach-based fluorescent light-up biosensors for multiplexed and label-free detection of microRNAs. Chem. Commun. 54:3010.
 Zinskieet al. (2018) Live-cell imaging of small nucleolar RNA tagged with the broccoli aptamer in yeast. Chem. Commun. 54:3010.
 Masuda et al. (2017) A genetically encoded fluorescent tRNA is active in live cell protein synthesis. Nucleic Acids Res. 45 (7):4081.
 Warner et al. (2017) A homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nat. Chem. Biol. 13 (11):1195.